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From: Richard C. <ric...@ea...> - 2008-10-13 14:27:48
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Thank you Irene I am not even sure 'how' to reply to forum responses such as yours ... do I reply directly to you ? So I assume that one cannot have a training file of mixed types ??? i.e., one column of integer, one column of names, another of integer, another of names ??? -- richard ----- Original Message ----- From: Irene Kouskoumvekaki To: dat...@li... Sent: Monday, October 13, 2008 12:48 AM Subject: Re: [Databionic-ESOM-User] Need help with .NAMES files Hi Richard, I have attached here a .name file to show you how it should look like. Basically you write in the first row the total number of data and then the first column is an index and the second one the name. In the attached file there are 20 wine samples divided into 3 classes: red, white and rose. Hope it helps. /Irene From: Richard Clements [mailto:ric...@ea...] Sent: Sunday, October 12, 2008 9:52 PM To: dat...@li... Subject: [Databionic-ESOM-User] Need help with .NAMES files I am new to eSOM. I do not understand when, how to use the .NAMES file option. WHere can I find a real sample-reference file of .NAMES type ?? ( to check format ) How can I save a file within eSOM as a .NAMES type ?? thank you for your patience. DeSio __________ Information from ESET NOD32 Antivirus, version of virus signature database 3517 (20081013) __________ The message was checked by ESET NOD32 Antivirus. http://www.eset.com ------------------------------------------------------------------------------ ------------------------------------------------------------------------- This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK & win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100&url=/ __________ Information from ESET NOD32 Antivirus, version of virus signature database 3517 (20081013) __________ The message was checked by ESET NOD32 Antivirus. http://www.eset.com ------------------------------------------------------------------------------ _______________________________________________ Databionic-ESOM-User mailing list Dat...@li... https://lists.sourceforge.net/lists/listinfo/databionic-esom-user __________ Information from ESET NOD32 Antivirus, version of virus signature database 3517 (20081013) __________ The message was checked by ESET NOD32 Antivirus. http://www.eset.com |
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From: Richard C. <ric...@ea...> - 2008-10-12 18:52:13
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I am new to eSOM. I do not understand when, how to use the .NAMES file option. WHere can I find a real sample-reference file of .NAMES type ?? ( to check format ) How can I save a file within eSOM as a .NAMES type ?? thank you for your patience. DeSio |
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From: Fabian M. <fa...@my...> - 2008-08-12 01:23:52
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Hi, can you please explain why you think only 3 digits would be supported? The IO classes use the standard java.text.NumberFormat for parsing. This is initialized with the local of your Java virtual machine. Maybe there are some problems with the configuration of your JVM? fabian P.S. z-transform projects to zero mean and unit variance, not [-1, 1] (which is available as well). Niko Efthymiou wrote: > On 0, Slimane OULAD NAOUI <oul...@ya...> wrote: > >> hi, >> by this mail, i notice you the problem of number precision in >> your tool. my data set include vectors of numbers with 6 digits after the decimal >> separator. but if i 'm correct the tool load the data truncated only to >> 3 digits decimals precision (ex: 0.001452 is represented as 0 !). >> i expose this pb, hope for any guides >> thanks in advances >> > > Hi, > > unfortunately I can't help you much, but the place where you may want to > look is LrnFile.java. > > Other than this, ESOM works best with data normalized to the interval > [-1,1]. The is a z-transform tool somewhere in the GUI that can do this > for you. > > Greets Niko > > ------------------------------------------------------------------------- > This SF.Net email is sponsored by the Moblin Your Move Developer's challenge > Build the coolest Linux based applications with Moblin SDK & win great prizes > Grand prize is a trip for two to an Open Source event anywhere in the world > http://moblin-contest.org/redirect.php?banner_id=100&url=/ > _______________________________________________ > Databionic-ESOM-User mailing list > Dat...@li... > https://lists.sourceforge.net/lists/listinfo/databionic-esom-user > > > |
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From: Niko E. <ne...@ne...> - 2008-08-10 11:25:53
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On 0, Slimane OULAD NAOUI <oul...@ya...> wrote: > hi, > by this mail, i notice you the problem of number precision in > your tool. my data set include vectors of numbers with 6 digits after the decimal > separator. but if i 'm correct the tool load the data truncated only to > 3 digits decimals precision (ex: 0.001452 is represented as 0 !). > i expose this pb, hope for any guides > thanks in advances Hi, unfortunately I can't help you much, but the place where you may want to look is LrnFile.java. Other than this, ESOM works best with data normalized to the interval [-1,1]. The is a z-transform tool somewhere in the GUI that can do this for you. Greets Niko |
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From: Slimane O. N. <oul...@ya...> - 2008-08-06 12:20:55
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hi,
by this mail, i notice you the problem of number precision in
your tool. my data set include vectors of numbers with 6 digits after the decimal
separator. but if i 'm correct the tool load the data truncated only to
3 digits decimals precision (ex: 0.001452 is represented as 0 !).
i expose this pb, hope for any guides
thanks in advances
_____________________________________________________________________________
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From: Irene K. <ir...@cb...> - 2008-07-23 13:08:38
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That was exactly what I needed! Thanks Irene -----Original Message----- From: dat...@li... [mailto:dat...@li...] On Behalf Of Niko Efthymiou Sent: Wednesday, July 23, 2008 3:04 PM To: dat...@li... Subject: Re: [Databionic-ESOM-User] data behind best-matches On 0, Irene Kouskoumvekaki <ir...@cb...> wrote: > When I say mixed neurons (or best-matches), I mean neurons that are > best-matches to items that belong to both my pre-assigned classes. It must > be somehow possible to retrieve this information from the map, because it is > something that you can do by simply clicking on each best-match, one at a > time. I just want to do it in a high-throughput way. But maybe you are right > and I need to write a code for that... Now I understand :) Well then can take the .bm file [1]. Sort it, according to the second and third column and look at adjacent lines.. If the second and third column are equal with the next/previous line, then the data points (index is in the first column) have the same bestmatch. If you need something more sophisticated you can take a look at the Java-API [2]. I'm sure there will be a way to get the data point for a best match somewhere. Unfortunately its been quite a while, and I can't give you a direct pointer, but I'd start by looking at the BMInfoPanel class. [1] http://databionic-esom.sourceforge.net/user.html#File_formats [2] http://databionic-esom.sourceforge.net/devel.html ------------------------------------------------------------------------- This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK & win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100&url=/ _______________________________________________ Databionic-ESOM-User mailing list Dat...@li... https://lists.sourceforge.net/lists/listinfo/databionic-esom-user |
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From: Niko E. <ne...@ne...> - 2008-07-23 13:05:25
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On 0, Irene Kouskoumvekaki <ir...@cb...> wrote: > When I say mixed neurons (or best-matches), I mean neurons that are > best-matches to items that belong to both my pre-assigned classes. It must > be somehow possible to retrieve this information from the map, because it is > something that you can do by simply clicking on each best-match, one at a > time. I just want to do it in a high-throughput way. But maybe you are right > and I need to write a code for that... Now I understand :) Well then can take the .bm file [1]. Sort it, according to the second and third column and look at adjacent lines.. If the second and third column are equal with the next/previous line, then the data points (index is in the first column) have the same bestmatch. If you need something more sophisticated you can take a look at the Java-API [2]. I'm sure there will be a way to get the data point for a best match somewhere. Unfortunately its been quite a while, and I can't give you a direct pointer, but I'd start by looking at the BMInfoPanel class. [1] http://databionic-esom.sourceforge.net/user.html#File_formats [2] http://databionic-esom.sourceforge.net/devel.html |
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From: Irene K. <ir...@cb...> - 2008-07-23 12:38:46
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When I say mixed neurons (or best-matches), I mean neurons that are best-matches to items that belong to both my pre-assigned classes. It must be somehow possible to retrieve this information from the map, because it is something that you can do by simply clicking on each best-match, one at a time. I just want to do it in a high-throughput way. But maybe you are right and I need to write a code for that... -----Original Message----- From: dat...@li... [mailto:dat...@li...] On Behalf Of Niko Efthymiou Sent: Wednesday, July 23, 2008 1:33 PM To: dat...@li... Subject: Re: [Databionic-ESOM-User] data behind best-matches On 0, Irene Kouskoumvekaki <ir...@cb...> wrote: > Well, I want to avoid manual classification and I am not interested in that > anyway. I just want to see where esom is placing the items of the dataset > during training. Seeing into the mixed neurons will give me an idea of what > percentage of each of my two classes is VERY similar to each other. If I > won't include the class information during training, I will still have the > same problem, as long as I cannot retrieve a list of all items sharing the > same best-match. Well the neurons don't belong to class. So there are no mixed neurons. That said, you want the nearest data point on the ESOM for each data point. Am I correct? Without writing some Code you are probably out of luck. You could however do a flood-fill on the weight matrix starting at each Data point best match and stopping as soon as you find another best match. Or something like that... That said, I am not sure that ESOM, is the right tool for your job. You will probably have very similar results if you just calculate all euclidean distances for each data point and take the lowest. Fabian, what do you think? Greets Niko ------------------------------------------------------------------------- This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK & win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100&url=/ _______________________________________________ Databionic-ESOM-User mailing list Dat...@li... https://lists.sourceforge.net/lists/listinfo/databionic-esom-user |
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From: Niko E. <ne...@ne...> - 2008-07-23 11:34:18
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On 0, Irene Kouskoumvekaki <ir...@cb...> wrote: > Well, I want to avoid manual classification and I am not interested in that > anyway. I just want to see where esom is placing the items of the dataset > during training. Seeing into the mixed neurons will give me an idea of what > percentage of each of my two classes is VERY similar to each other. If I > won't include the class information during training, I will still have the > same problem, as long as I cannot retrieve a list of all items sharing the > same best-match. Well the neurons don't belong to class. So there are no mixed neurons. That said, you want the nearest data point on the ESOM for each data point. Am I correct? Without writing some Code you are probably out of luck. You could however do a flood-fill on the weight matrix starting at each Data point best match and stopping as soon as you find another best match. Or something like that... That said, I am not sure that ESOM, is the right tool for your job. You will probably have very similar results if you just calculate all euclidean distances for each data point and take the lowest. Fabian, what do you think? Greets Niko |
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From: Irene K. <ir...@cb...> - 2008-07-23 11:04:01
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\\Actually the color depends on whatever your .cls file contained before training. So areas with mixed colors just mean, that your classification does not agree with the ESOM's. To actually classify with an ESOM you have so select the areas that are surrounded by "mountains" on the map by hand and assign them Classes. Well, I want to avoid manual classification and I am not interested in that anyway. I just want to see where esom is placing the items of the dataset during training. Seeing into the mixed neurons will give me an idea of what percentage of each of my two classes is VERY similar to each other. If I won't include the class information during training, I will still have the same problem, as long as I cannot retrieve a list of all items sharing the same best-match. \\I'm not really sure what you are doing. It could be a bug or maybe you are just doing something wrong... But I think you are confusing Training (= the generation of the map) and classification (= what you have to do after the map is trained). Classification with ESOM is a manual process. I agree completely. I am just trying different things to see the output I get... Is it possible to view as colored points the items on the map, instead of the best-matches? |
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From: Niko E. <ne...@ne...> - 2008-07-23 10:46:52
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On 0, Irene Kouskoumvekaki <ir...@cb...> wrote: > Thank you Fabian, > Let me try to explain it a bit better. At the end of > the training I end up with a map with best-matches colored as class 1 > and best-matches colored class 2. However, if I select an area that > contains only best-matches of one color, I can see that it contains > compounds of both classes (so, I guess that the color depends on which > of the two has the majority). Actually the color depends on whatever your .cls file contained before training. So areas with mixed colors just mean, that your classification does not agree with the ESOM's. To actually classify with an ESOM you have so select the areas that are surrounded by "mountains" on the map by hand and assign them Classes. > So, I want to see how many of the compounds of class 2 are found under > best-matches colored as class 1 (and vice versa). Or, in other words, > how many mixed neurons my map has and how many compounds of each class > are found in the mixed neurons. Well what you probably want to do is, train a Map without a .cls file (it isn't used in the training anyway, but you can avoid getting biased by the colors ;). Classify your data according to the "mountain lines" on the map. Save the .cls file and then compare it with the original. There is a "save .cls" in the file menu, if I recall correctly. > If I do classification of the same dataset on the trained map and then save > the .cls file, this file is exactly the same as the original one. And the > only new file that is created during the classification is a projected.bm, > with the coordinates of the dataset on the map, which of course is the same > as the original .bm file, as I am using the same dataset. Am I doing > something wrong here? I'm not really sure what you are doing. It could be a bug or maybe you are just doing something wrong... But I think you are confusing Training (= the generation of the map) and classification (= what you have to do after the map is trained). Classification with ESOM is a manual process. Greets, Niko |
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From: Irene K. <ir...@cb...> - 2008-07-23 10:13:13
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Thank you Fabian, Let me try to explain it a bit better. At the end of the training I end up with a map with best-matches colored as class 1 and best-matches colored class 2. However, if I select an area that contains only best-matches of one color, I can see that it contains compounds of both classes (so, I guess that the color depends on which of the two has the majority). So, I want to see how many of the compounds of class 2 are found under best-matches colored as class 1 (and vice versa). Or, in other words, how many mixed neurons my map has and how many compounds of each class are found in the mixed neurons. If I do classification of the same dataset on the trained map and then save the .cls file, this file is exactly the same as the original one. And the only new file that is created during the classification is a projected.bm, with the coordinates of the dataset on the map, which of course is the same as the original .bm file, as I am using the same dataset. Am I doing something wrong here? best, Irene -----Original Message----- From: dat...@li... [mailto:dat...@li...] On Behalf Of Fabian Mörchen Sent: Wednesday, July 23, 2008 2:14 AM To: dat...@li... Subject: Re: [Databionic-ESOM-User] data behind best-matches Irene, I'm not sure if I understand correctly. If you have predefined classes, you already have the assignment of data examples to classes in the *.cls file you loaded. If you create a new classification based on a trained ESOM you can also save this to a *.cls file that stores data example id <-> class if pairs. Note, that ESOM training does not make use of any prior class information as it is an unsupervised algorithm. bye fabian Irene Kouskoumvekaki wrote: > > Hi, > > > > I have a list of items assigned into two classes. I train ESOM and the > produced map shows best-matches of the two colors, depending on the > pre-assigned class of the majority of the items that it is best-match > to (as I understand it). I would now like to create a list of the > items that are behind the best-matches of color 1 and those behind the > best-matches of color 2. Is this possible? > > Thanks > > Irene > > > > > > ------------------------------------------------------------------------ > > ------------------------------------------------------------------------- > This SF.Net email is sponsored by the Moblin Your Move Developer's challenge > Build the coolest Linux based applications with Moblin SDK & win great prizes > Grand prize is a trip for two to an Open Source event anywhere in the world > http://moblin-contest.org/redirect.php?banner_id=100&url=/ > ------------------------------------------------------------------------ > > _______________________________________________ > Databionic-ESOM-User mailing list > Dat...@li... > https://lists.sourceforge.net/lists/listinfo/databionic-esom-user > ------------------------------------------------------------------------- This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK & win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100&url=/ _______________________________________________ Databionic-ESOM-User mailing list Dat...@li... https://lists.sourceforge.net/lists/listinfo/databionic-esom-user |
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From: Niko E. <ne...@ne...> - 2008-07-23 09:47:22
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On 0, Slimane OULAD NAOUI <oul...@ya...> wrote: > Hi, > i am a CS student and i have to implement a clustering solution in web usage mining framework. > i found your consistant & interesting tool. and first would like to encourage you for this important work. > i trained the tool with relatively the same data set and have 6 clusters on result. my question is how the number of clusters is determined. and if there is a method to interpret this result > Hi, well the number of clusters depends mostly on your data. As to the interpretation you have to look at the cluster-data. What do the have in common that other clusters have not. It might be useful to check the component maps, to see which component is dominant in a particular part of the map. Greets, Niko |
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From: Slimane O. N. <oul...@ya...> - 2008-07-23 09:32:05
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Hi,
i am a CS student and i have to implement a clustering solution in web usage mining framework.
i found your consistant & interesting tool. and first would like to encourage you for this important work.
i trained the tool with relatively the same data set and have 6 clusters on result. my question is how the number of clusters is determined. and if there is a method to interpret this result
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From: Fabian M. <fa...@my...> - 2008-07-23 00:14:33
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Irene, I'm not sure if I understand correctly. If you have predefined classes, you already have the assignment of data examples to classes in the *.cls file you loaded. If you create a new classification based on a trained ESOM you can also save this to a *.cls file that stores data example id <-> class if pairs. Note, that ESOM training does not make use of any prior class information as it is an unsupervised algorithm. bye fabian Irene Kouskoumvekaki wrote: > > Hi, > > > > I have a list of items assigned into two classes. I train ESOM and the > produced map shows best-matches of the two colors, depending on the > pre-assigned class of the majority of the items that it is best-match > to (as I understand it). I would now like to create a list of the > items that are behind the best-matches of color 1 and those behind the > best-matches of color 2. Is this possible? > > Thanks > > Irene > > > > > > ------------------------------------------------------------------------ > > ------------------------------------------------------------------------- > This SF.Net email is sponsored by the Moblin Your Move Developer's challenge > Build the coolest Linux based applications with Moblin SDK & win great prizes > Grand prize is a trip for two to an Open Source event anywhere in the world > http://moblin-contest.org/redirect.php?banner_id=100&url=/ > ------------------------------------------------------------------------ > > _______________________________________________ > Databionic-ESOM-User mailing list > Dat...@li... > https://lists.sourceforge.net/lists/listinfo/databionic-esom-user > |
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From: Irene K. <ir...@cb...> - 2008-07-22 14:57:07
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Hi, I have a list of items assigned into two classes. I train ESOM and the produced map shows best-matches of the two colors, depending on the pre-assigned class of the majority of the items that it is best-match to (as I understand it). I would now like to create a list of the items that are behind the best-matches of color 1 and those behind the best-matches of color 2. Is this possible? Thanks Irene |
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From: Marcela <ho...@ya...> - 2008-06-26 01:35:57
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I want to be registered Marcela . __________________________________________________ Correo Yahoo! Espacio para todos tus mensajes, antivirus y antispam ¡gratis! Regístrate ya - http://correo.espanol.yahoo.com/ |
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From: Fabian M. <fa...@my...> - 2008-05-22 22:44:11
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Frederic, so you have 30-60 dimensional vectors with counts, similar to a histogram. in this case I would say that the used method to interpolate vectors makes sense and can be used together with sorensen. Do you think you are able to add this with some guidance? fabian rimet frederic wrote: > > Dear Fabian, > > My data are botanical data (counts of phytoplanctonic species in a > lake). Each sample of water is characterised by several algae species > (about 30 to 60 species) and for each species correspond a number of > cells. > > I'm not sure that Hamming distances can be used for my data (never > seen an example in litterature using the kind of distance), usually > Sorensen distances are used. > > It would be really nice to add Sorensen distances in the Databionics > ESOM analyser (when using the training tool in the data space distance > function menu). > > Thanks for your help, > > Frederic > > > > ----- Message d'origine ---- > De : "dat...@li..." > <dat...@li...> > À : dat...@li... > Envoyé le : Dimanche, 18 Mai 2008, 21h20mn 43s > Objet : Databionic-ESOM-User Digest, Vol 12, Issue 3 > > Send Databionic-ESOM-User mailing list submissions to > dat...@li... > <mailto:dat...@li...> > > To subscribe or unsubscribe via the World Wide Web, visit > https://lists.sourceforge.net/lists/listinfo/databionic-esom-user > or, via email, send a message with subject or body 'help' to > dat...@li... > <mailto:dat...@li...> > > You can reach the person managing the list at > dat...@li... > <mailto:dat...@li...> > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Databionic-ESOM-User digest..." > > > Today's Topics: > > 1. Re: Bray-Curtis distances (Fabian M?rchen) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Sat, 17 May 2008 21:40:44 -0400 > From: Fabian M?rchen <fa...@my... <mailto:fa...@my...>> > Subject: Re: [Databionic-ESOM-User] Bray-Curtis distances > To: dat...@li... > <mailto:dat...@li...> > Message-ID: <482...@my... > <mailto:482...@my...>> > Content-Type: text/plain; charset=ISO-8859-1 > > Frederic, > > Bray Curtis could be added very easily as it is already implemented in > colt. > > The Jaccard distance measures the difference between sets whereas the > ESOM works with numeric vectors. what does your input look like? do you > have categoric vectors represented as real numbers? > > Please note that for a meaningful ESOM training you need a distance > function for your vectors and the (weighted) mean of you input vectors > must represent an 'average' of the examples. This might not be the case > for categoric data depending on the encoding. A binary encoding might > work. > > A little while ago I added the hamming distance per special request. > Hamming is defined for binary vectors. The ESOM training generated > vectors using the default weighted mean but the distance function > rounds each entry to the nearest integer and counts the number of > identical entries in the two vectors. > > best > fabian > > Niko Efthymiou wrote: > > On Wednesday 14 May 2008, rimet frederic wrote: > > > >> Hello, > >> I've tried your eSOM program on ecological data (phytoplancton counts > >> of a french lake). It produces interesting maps and groups. > >> Nevertheless I wanted to know if you plan to add in the data space > >> distance function other distances more adapted to ecological data, as > >> for instance Sorensen (Bray & Curtis) Distance or Jaccard Distance ? > >> Thanks for your answer, > >> Fr?d?ric RIMET > >> > > > > Hello, > > > > as far as I know there are no such plans. However adding this metrics > > should not be wery hard. You just have to implement them as > > > > cern.colt.function.ThresholdVectorVectorFunction > > cern.colt.function.VectorVectorFunction > > > > objects and add them to > > > > databionics.math.DistanceFactory > > databionics.esom.Train > > > > and that schould be about it (my crystal ball reads ~100 lines of > code). > > Please consider submiting a patch if you do add them. > > > > > > Greats Niko > > > > > ------------------------------------------------------------------------- > > This SF.net email is sponsored by: Microsoft > > Defy all challenges. Microsoft(R) Visual Studio 2008. > > http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/ > > _______________________________________________ > > Databionic-ESOM-User mailing list > > Dat...@li... > <mailto:Dat...@li...> > > https://lists.sourceforge.net/lists/listinfo/databionic-esom-user > > > > > > > > > > > ------------------------------ > > ------------------------------------------------------------------------- > This SF.net email is sponsored by: Microsoft > Defy all challenges. Microsoft(R) Visual Studio 2008. > http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/ > > ------------------------------ > > _______________________________________________ > Databionic-ESOM-User mailing list > Dat...@li... > <mailto:Dat...@li...> > https://lists.sourceforge.net/lists/listinfo/databionic-esom-user > > > End of Databionic-ESOM-User Digest, Vol 12, Issue 3 > *************************************************** > > __________________________________________________ > Do You Yahoo!? > En finir avec le spam? Yahoo! Mail vous offre la meilleure protection > possible contre les messages non sollicités > http://mail.yahoo.fr Yahoo! Mail > ------------------------------------------------------------------------ > > ------------------------------------------------------------------------- > This SF.net email is sponsored by: Microsoft > Defy all challenges. Microsoft(R) Visual Studio 2008. > http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/ > ------------------------------------------------------------------------ > > _______________________________________________ > Databionic-ESOM-User mailing list > Dat...@li... > https://lists.sourceforge.net/lists/listinfo/databionic-esom-user > |
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From: rimet f. <rim...@ya...> - 2008-05-22 19:26:35
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Dear Fabian, My data are botanical data (counts of phytoplanctonic species in a lake). Each sample of water is characterised by several algae species (about 30 to 60 species) and for each species correspond a number of cells. I'm not sure that Hamming distances can be used for my data (never seen an example in litterature using the kind of distance), usually Sorensen distances are used. It would be really nice to add Sorensen distances in the Databionics ESOM analyser (when using the training tool in the data space distance function menu). Thanks for your help, Frederic ----- Message d'origine ---- De : "dat...@li..." <dat...@li...> À : dat...@li... Envoyé le : Dimanche, 18 Mai 2008, 21h20mn 43s Objet : Databionic-ESOM-User Digest, Vol 12, Issue 3 Send Databionic-ESOM-User mailing list submissions to dat...@li... To subscribe or unsubscribe via the World Wide Web, visit https://lists.sourceforge.net/lists/listinfo/databionic-esom-user or, via email, send a message with subject or body 'help' to dat...@li... You can reach the person managing the list at dat...@li... When replying, please edit your Subject line so it is more specific than "Re: Contents of Databionic-ESOM-User digest..." Today's Topics: 1. Re: Bray-Curtis distances (Fabian M?rchen) ---------------------------------------------------------------------- Message: 1 Date: Sat, 17 May 2008 21:40:44 -0400 From: Fabian M?rchen <fa...@my...> Subject: Re: [Databionic-ESOM-User] Bray-Curtis distances To: dat...@li... Message-ID: <482...@my...> Content-Type: text/plain; charset=ISO-8859-1 Frederic, Bray Curtis could be added very easily as it is already implemented in colt. The Jaccard distance measures the difference between sets whereas the ESOM works with numeric vectors. what does your input look like? do you have categoric vectors represented as real numbers? Please note that for a meaningful ESOM training you need a distance function for your vectors and the (weighted) mean of you input vectors must represent an 'average' of the examples. This might not be the case for categoric data depending on the encoding. A binary encoding might work. A little while ago I added the hamming distance per special request. Hamming is defined for binary vectors. The ESOM training generated vectors using the default weighted mean but the distance function rounds each entry to the nearest integer and counts the number of identical entries in the two vectors. best fabian Niko Efthymiou wrote: > On Wednesday 14 May 2008, rimet frederic wrote: > >> Hello, >> I've tried your eSOM program on ecological data (phytoplancton counts >> of a french lake). It produces interesting maps and groups. >> Nevertheless I wanted to know if you plan to add in the data space >> distance function other distances more adapted to ecological data, as >> for instance Sorensen (Bray & Curtis) Distance or Jaccard Distance ? >> Thanks for your answer, >> Fr?d?ric RIMET >> > > Hello, > > as far as I know there are no such plans. However adding this metrics > should not be wery hard. You just have to implement them as > > cern.colt.function.ThresholdVectorVectorFunction > cern.colt.function.VectorVectorFunction > > objects and add them to > > databionics.math.DistanceFactory > databionics.esom.Train > > and that schould be about it (my crystal ball reads ~100 lines of code). > Please consider submiting a patch if you do add them. > > > Greats Niko > > ------------------------------------------------------------------------- > This SF.net email is sponsored by: Microsoft > Defy all challenges. Microsoft(R) Visual Studio 2008. > http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/ > _______________________________________________ > Databionic-ESOM-User mailing list > Dat...@li... > https://lists.sourceforge.net/lists/listinfo/databionic-esom-user > > > ------------------------------ ------------------------------------------------------------------------- This SF.net email is sponsored by: Microsoft Defy all challenges. Microsoft(R) Visual Studio 2008. http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/ ------------------------------ _______________________________________________ Databionic-ESOM-User mailing list Dat...@li... https://lists.sourceforge.net/lists/listinfo/databionic-esom-user End of Databionic-ESOM-User Digest, Vol 12, Issue 3 *************************************************** __________________________________________________ Do You Yahoo!? En finir avec le spam? Yahoo! Mail vous offre la meilleure protection possible contre les messages non sollicités http://mail.yahoo.fr Yahoo! Mail |
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From: Fabian M. <fa...@my...> - 2008-05-18 01:40:57
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Frederic, Bray Curtis could be added very easily as it is already implemented in colt. The Jaccard distance measures the difference between sets whereas the ESOM works with numeric vectors. what does your input look like? do you have categoric vectors represented as real numbers? Please note that for a meaningful ESOM training you need a distance function for your vectors and the (weighted) mean of you input vectors must represent an 'average' of the examples. This might not be the case for categoric data depending on the encoding. A binary encoding might work. A little while ago I added the hamming distance per special request. Hamming is defined for binary vectors. The ESOM training generated vectors using the default weighted mean but the distance function rounds each entry to the nearest integer and counts the number of identical entries in the two vectors. best fabian Niko Efthymiou wrote: > On Wednesday 14 May 2008, rimet frederic wrote: > >> Hello, >> I've tried your eSOM program on ecological data (phytoplancton counts >> of a french lake). It produces interesting maps and groups. >> Nevertheless I wanted to know if you plan to add in the data space >> distance function other distances more adapted to ecological data, as >> for instance Sorensen (Bray & Curtis) Distance or Jaccard Distance ? >> Thanks for your answer, >> Frédéric RIMET >> > > Hello, > > as far as I know there are no such plans. However adding this metrics > should not be wery hard. You just have to implement them as > > cern.colt.function.ThresholdVectorVectorFunction > cern.colt.function.VectorVectorFunction > > objects and add them to > > databionics.math.DistanceFactory > databionics.esom.Train > > and that schould be about it (my crystal ball reads ~100 lines of code). > Please consider submiting a patch if you do add them. > > > Greats Niko > > ------------------------------------------------------------------------- > This SF.net email is sponsored by: Microsoft > Defy all challenges. Microsoft(R) Visual Studio 2008. > http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/ > _______________________________________________ > Databionic-ESOM-User mailing list > Dat...@li... > https://lists.sourceforge.net/lists/listinfo/databionic-esom-user > > > |
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From: Niko E. <ne...@Ma...> - 2008-05-14 21:45:21
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On Wednesday 14 May 2008, rimet frederic wrote: > Hello, > I've tried your eSOM program on ecological data (phytoplancton counts > of a french lake). It produces interesting maps and groups. > Nevertheless I wanted to know if you plan to add in the data space > distance function other distances more adapted to ecological data, as > for instance Sorensen (Bray & Curtis) Distance or Jaccard Distance ? > Thanks for your answer, > Frédéric RIMET Hello, as far as I know there are no such plans. However adding this metrics should not be wery hard. You just have to implement them as cern.colt.function.ThresholdVectorVectorFunction cern.colt.function.VectorVectorFunction objects and add them to databionics.math.DistanceFactory databionics.esom.Train and that schould be about it (my crystal ball reads ~100 lines of code). Please consider submiting a patch if you do add them. Greats Niko |
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From: rimet f. <rim...@ya...> - 2008-05-14 15:01:58
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Hello, I've tried your eSOM program on ecological data (phytoplancton counts of a french lake). It produces interesting maps and groups. Nevertheless I wanted to know if you plan to add in the data space distance function other distances more adapted to ecological data, as for instance Sorensen (Bray & Curtis) Distance or Jaccard Distance ? Thanks for your answer, Frédéric RIMET __________________________________________________ Do You Yahoo!? En finir avec le spam? Yahoo! Mail vous offre la meilleure protection possible contre les messages non sollicités http://mail.yahoo.fr Yahoo! Mail |
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From: Niko E. <ne...@Ma...> - 2008-04-06 15:45:02
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Hello, On Saturday 05 April 2008, Eng. Hisham Abdel Maguid wrote: > We are looking to promote that software in various sectors, so I > thought of contacting you for that matter. It is a new concept in > viewing statistics and trends in an animated way, it is called > Trendanalyzer. It could be used in analysis,research, decision > making, presentation,etc. I took a look at the site, but I din't find anything technical about your new concept? Could you elaborate a bit on your concept? Fourther how does it corelate to the ESOM-Tools? > Here is one link for part of what we did with the Egyptian Government > : www.epicsyst.com/visual.swf > > Here is another link for a project we did with Princeton University > on US unemployment : > > www.epicsyst.com/main5.swf And what are those supposed to tell me? What knowledge to the comunicate better than other methods? Don't get me wrong, but there is plenty of funky animations and no text describing what I am supposed to see there... Greetings, Niko |
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From: Eng. H. A. M. <hi...@ep...> - 2008-04-05 16:16:41
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Dear Sir, Epic Systems together with Beemode (www.beemode.com) has developed a Data Visualisation software almost ready to be released soon. It does the same functions as Gapminder which was invented by a Swedish Professor and was bought by Google 1 year ago. Google never released it. You can view it : - www.gapminder.org We are looking to promote that software in various sectors, so I thought of contacting you for that matter. It is a new concept in viewing statistics and trends in an animated way, it is called Trendanalyzer. It could be used in analysis,research, decision making, presentation,etc. Here is one link for part of what we did with the Egyptian Government : www.epicsyst.com/visual.swf Here is another link for a project we did with Princeton University on US unemployment : www.epicsyst.com/main5.swf I hope you could evaluate it and give me your comments. So many ideas are there. Regards Eng. Hisham Abdel Maguid Managing Director Epic Systems www.epicsyst.com |
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From: <noe...@Ma...> - 2008-02-24 14:40:37
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Hello users of the Databionic ESOM Tools, we finally released the Databionic-ESOM Tools 1.1. A list of all included new Features and Bugfixes can be seen on http://databionic-esom.sourceforge.net/changes-report.html Best Regards Mario Nöcker |
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